title: Identification and analysis of novel microRNAs from fragile sites of human cervical cancer: computational and experimental approach.
abstract: Accurate identification of mature miRNAs is an important requirement for exploring the post-transcriptional regulatory mechanism of organisms. In this work we present a novel computational tool 'Mpred' which first identifies pre-miRNAs and then predicts its mature miRNAs. We first use our method to learn with high accuracy characteristic features of human miRNA precursors from miRbase registry and then apply to sequences from fragile site regions related to cervical cancer in search of novel miRNA genes. The study identified 13 putative miRNA-like sequences and most of them were not related to each other and do not share homology with annotated sequences. Finally, four of the top scoring predictions were verified experimentally using quantitative RT-PCR validation. Expression profile studies revealed that four novel miRs were present in cervical tissues and these data compiled here provide a regulatory framework of miRNA genes that may have roles in tumorigenesis.
authors.affiliation: Integrated Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India. reshmi@rgcb.res.in
authors.forename: G
authors.initials: G
authors.lastname: Reshmi
authors.forename: S S Vinod
authors.initials: SS
authors.lastname: Chandra
authors.forename: V Janki Mohan
authors.initials: VJ
authors.lastname: Babu
authors.forename: P S Saneesh
authors.initials: PS
authors.lastname: Babu
authors.forename: W S
authors.initials: WS
authors.lastname: Santhi
authors.forename: Surya
authors.initials: S
authors.lastname: Ramachandran
authors.forename: S
authors.initials: S
authors.lastname: Lakshmi
authors.forename: Achuthsankar S
authors.initials: AS
authors.lastname: Nair
authors.forename: M Radhakrishna
authors.initials: MR
authors.lastname: Pillai
mesh_terms: D001185:Artificial Intelligence; D001483:Base Sequence; D045744:Cell Line, Tumor; D003198:Computer Simulation; D005260:Female; D015972:Gene Expression Regulation, Neoplastic; D056726:Genetic Association Studies; D006801:Humans; D008390:Markov Chains; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012372:ROC Curve; D012984:Software; D002583:Uterine Cervical Neoplasms / Q000235:genetics* / Q000378:metabolism
chemical_list: D035683:MicroRNAs